housekeeping (#71)

* switch to ini file * save figs to test_dir * Revert "switch to ini file" This reverts commit 597fccc. * linting * workflows should trigger for changes to tests * specify dependency ranges (#70) * specify dependency ranges I ended up trying to install mud on a computer with an older scikit-learn, and it ended up using the cache of like version 0.something, so I want to at least specify the major version we require for the more important libraries. * loosen matplotlib * 3.7 support is a pain... * typo * prevent warnings from numpy * specify build os, tools * fix flake8 E721 errors * [black] lint files * [black] notebook linting * cover more versions of python * type-checking investigation (#68) * print mypy and python versions in workflow * 'if save_path' used to fix 10 mypy errors * automatic fix using https://github.com/hauntsaninja/no_implicit_optional * post-fix linting * refactor to address C901: too complex * refactor to address C901: too complex * ignore C901 * fix typo * sort imports * if save_path is not None * no more 3.12 bc numpy 1.24 * fix all mypy issues with 1.8.0 * enforce old cli functionality * actions updates, experiments with 3.12 (#72) * experiment with 3.12 * loosen pandas for 3.12 * build updates * rename, try new build
mathematicalmichael · Jan 22, 2024 · a9c5d5f · a9c5d5f
1 parent a134ca7
commit a9c5d5f
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -2,37 +2,39 @@ name: builds
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
     paths:
       - "src/**.py"
+      - "tests/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/build.yml"
   pull_request:
-    branches-ignore: '**docker**'
+    branches-ignore: ["**docker**"]
     paths:
       - "src/**.py"
+      - "tests/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/build.yml"
   schedule:
-      - cron: "0 0 1 * *"
+    - cron: "0 0 1 * *"
 
 jobs:
   build:
-    name: Test build process
+    name: packaging
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -42,7 +44,7 @@ jobs:
           pip install --upgrade wheel setuptools setuptools_scm
 
       - name: Inspect version info
-        run: | 
+        run: |
           python setup.py --version
           git describe --dirty --tags --long --match "*[0-9]*"
 
@@ -55,12 +57,15 @@ jobs:
         run: |
           pip install -e .
           pip uninstall -y mud
- 
+
       - name: Test build
         run: |
           python setup.py sdist bdist_wheel
-          pip uninstall -y mud
 
+      - name: New build
+        run: |
+          pip install build
+          python -m build --sdist --wheel
 
   style:
     name: Enforce style
@@ -70,12 +75,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 1
 
       - name: setup
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -94,4 +99,6 @@ jobs:
 
       - name: type checks
         run: |
+          python --version
+          mypy --version
           mypy src/mud/ tests/
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -5,13 +5,15 @@ on:
     branches: [ main ]
     paths:
       - "src/**.py"
+      - "tests/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/main.yml"
   pull_request:
-    branches-ignore: "**docker**"
+    branches-ignore: ["**docker**"]
     paths:
       - "src/**.py"
+      - "tests/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/main.yml"
@@ -20,19 +22,19 @@ on:
 
 jobs:
   unit-tests:
-    name: Run unit tests
+    name: pytest
     strategy:
       matrix:
-        python-version: ["3.7", "3.10"]
+        python-version: ["3.7", "3.10", "3.11", "3.12"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -45,25 +47,25 @@ jobs:
         run: pytest
 
       - name: Upload coverage to coveralls.io
-        if: ${{ matrix.python-version }} == 3.9
+        if: ${{ matrix.python-version }} == 3.10
         run: coveralls --service=github
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   integration-tests:
-    name: Run integration tests
+    name: cli examples
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10", "3.12"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 1
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -77,6 +79,7 @@ jobs:
             texlive-fonts-extra \
             texlive-science \
             latexmk \
+            dvipng \
             cm-super
 
       - name: Install Python dependencies
@@ -86,7 +89,7 @@ jobs:
           pip install .[examples]
 
       - name: Old CLI
-        continue-on-error: true
+        continue-on-error: false
         run: mud_run_all -v
 
       - name: New CLI

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -4,6 +4,11 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -18,7 +23,6 @@ formats:
   - epub
 
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: pip

diff --git a/notebooks/FenicsSolve.ipynb b/notebooks/FenicsSolve.ipynb
@@ -190,7 +190,6 @@
     "    gamma=-3,\n",
     "    save_data=True,\n",
     "):\n",
-    "\n",
     "    if len(mins) != len(maxs):\n",
     "        raise ValueError(\"min/max arrays must be of same length\")\n",
     "\n",

diff --git a/notebooks/MUD-ADCIRC-Figs.ipynb b/notebooks/MUD-ADCIRC-Figs.ipynb
@@ -3516,7 +3516,6 @@
     "    close_fig: bool = False,\n",
     "    dpi: int = 500,\n",
     "):\n",
-    "\n",
     "    triangles = mtri.Triangulation(\n",
     "        adcirc_grid_data[\"X\"], adcirc_grid_data[\"Y\"], adcirc_grid_data[\"triangles\"]\n",
     "    )\n",

diff --git a/notebooks/MUD_Butler_2021.ipynb b/notebooks/MUD_Butler_2021.ipynb
@@ -1915,7 +1915,6 @@
     "def plot_conv(\n",
     "    info, method=\"pca\", field=\"err\", agg=\"mean\", ax=None, fit=False, **kwargs\n",
     "):\n",
-    "\n",
     "    stat = info.groupby([\"type\", \"n\"])[field].aggregate([agg])\n",
     "    stat = stat.unstack(level=0)[(agg, method)]\n",
     "\n",

diff --git a/notebooks/Nonlinear_Examples.ipynb b/notebooks/Nonlinear_Examples.ipynb
@@ -200,7 +200,6 @@
     "    t_start=1.0,\n",
     "    sampling_freq=100.0,\n",
     "):\n",
-    "\n",
     "    time = np.linspace(time_range[0], time_range[1], 1000)\n",
     "    times = np.arange(t_start, time_range[1], 1 / sampling_freq)[0:N]\n",
     "\n",

diff --git a/notebooks/ODE_ExpDecay.ipynb b/notebooks/ODE_ExpDecay.ipynb
@@ -122,7 +122,6 @@
     "    sampling_freq=100.0,\n",
     "    std_dev=0.05,\n",
     "):\n",
-    "\n",
     "    u_t_lambda = lambda t, l: u_0 * np.exp(-np.outer(l, t))\n",
     "\n",
     "    # Build initial samples\n",
@@ -190,7 +189,6 @@
     "    sampling_freq=10.0,\n",
     "    std_dev=0.05,\n",
     "):\n",
-    "\n",
     "    u_t_lambda = lambda t, l1, l2: (l1 * np.exp(-np.outer(t, l2))).T\n",
     "\n",
     "    # Build initial samples\n",
@@ -619,7 +617,6 @@
     "    sampling_freq=10.0,\n",
     "    std_dev=0.05,\n",
     "):\n",
-    "\n",
     "    u_t_lambda = lambda t, l1, l2: (l1 * np.exp(-np.outer(t, l2))).T\n",
     "\n",
     "    # Build initial samples\n",

diff --git a/setup.cfg b/setup.cfg
@@ -32,10 +32,10 @@ package_dir =
 # Add here dependencies of your project (semicolon/line-separated), e.g.
 install_requires =
     importlib-metadata; python_version<"3.10"
-    numpy>=1.20
-    scipy
-    matplotlib
-    scikit-learn
+    numpy>=1.20,<1.27
+    scipy>=1.2,<2.0
+    matplotlib>=1.0,<4.0
+    scikit-learn>=1.0,<2.0
 
 # Require a specific Python version, e.g. Python 2.7 or >= 3.4
 python_requires = >=3.7
@@ -67,7 +67,7 @@ examples =
     click
     tqdm
     prettytable
-    pandas
+    pandas>=1.2,<3.0
     wget